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* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/
@ 2020-10-24  4:31 Horea Christian
  0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2020-10-24  4:31 UTC (permalink / raw
  To: gentoo-commits

commit:     83fd8b496d322f3f6130ff251f0567486f35a14a
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Oct 24 04:31:12 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Oct 24 04:31:12 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=83fd8b49

sci-biology/afni: fixed build issues for systems missing python 2.7

Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/afni/afni-20.1.16.ebuild             |  6 +++++-
 sci-biology/afni/files/afni-20.1.16-python.patch | 11 +++++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
index 4953408d6..09e2b7def 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -39,6 +39,10 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 BUILD="linux_fedora_19_64"
 BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
 
+PATCHES=(
+	"${FILESDIR}/${P}-python.patch"
+)
+
 src_prepare() {
 	find -type f -exec sed -i -e "s/-lXp //g" {} +
 	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
@@ -56,7 +60,7 @@ src_prepare() {
 		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
 		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
 	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
-	eapply_user
+	default
 }
 
 src_compile() {

diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch
new file mode 100644
index 000000000..24ed98405
--- /dev/null
+++ b/sci-biology/afni/files/afni-20.1.16-python.patch
@@ -0,0 +1,11 @@
+--- a/other_builds/Makefile.linux_fedora_19_64      2020-10-09 07:07:58.348874414 -0400
++++ b/other_builds/Makefile.linux_fedora_19_64	2020-10-10 01:15:22.337755934 -0400
+@@ -11,8 +11,6 @@
+
+ # ------------------------------
+ # python from C
+-IPYTHON  = -DSELENIUM_READY -I/usr/include/python2.7
+-LDPYTHON = -lpython2.7
+
+ # ----------------------------------------------------------------------
+ # X configuration


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/
@ 2022-01-25 15:34 Andrew Ammerlaan
  0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 15:34 UTC (permalink / raw
  To: gentoo-commits

commit:     7c2d62f11603cc64279a72f03d2b7b18d61b9de0
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 15:34:00 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 15:34:00 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7c2d62f1

sci-biology/afni: bump to version 22.0.03

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/afni/afni-19.3.12.ebuild               | 72 --------------------
 sci-biology/afni/afni-20.3.03.ebuild               | 77 ----------------------
 .../{afni-20.1.16.ebuild => afni-22.0.03.ebuild}   | 24 +++----
 sci-biology/afni/afni-9999.ebuild                  | 70 --------------------
 sci-biology/afni/files/afni-20.1.16-python.patch   | 11 ----
 sci-biology/afni/files/afni-20.3.03-python.patch   | 11 ----
 6 files changed, 10 insertions(+), 255 deletions(-)

diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-19.3.12.ebuild
deleted file mode 100644
index db19930fd..000000000
--- a/sci-biology/afni/afni-19.3.12.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
-	media-libs/glu
-	media-libs/netpbm
-	media-libs/qhull
-	media-video/mpeg-tools
-	sci-libs/gsl
-	sys-devel/llvm:*
-	virtual/jpeg:0
-	x11-libs/libGLw
-	x11-libs/libXft
-	x11-libs/libXi
-	x11-libs/libXpm
-	x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-	app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
-	find -type f -exec sed -i -e "s/-lXp //g" {} +
-	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
-	# Unbundle imcat
-	sed -e "s/ imcat / /g" \
-		-i Makefile.INCLUDE || die "Could not edit includes files."
-	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
-		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
-		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-		-i Makefile || die "Could not edit Makefile"
-		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
-		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
-	eapply_user
-}
-
-src_compile() {
-	emake -j1 all plugins suma_exec
-}
-
-src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
-	emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
-	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}"
-	done
-}

diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
deleted file mode 100644
index 3185a297a..000000000
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
-	media-libs/glu
-	media-libs/netpbm
-	media-libs/qhull
-	media-video/mpeg-tools
-	sci-libs/gsl
-	sys-devel/llvm:*
-	virtual/jpeg:0
-	x11-libs/libGLw
-	x11-libs/libXft
-	x11-libs/libXi
-	x11-libs/libXpm
-	x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-	app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-#PATCHES=(
-#	"${FILESDIR}/${P}-python.patch"
-#)
-
-src_prepare() {
-	eapply "${FILESDIR}/${P}-python.patch" || die
-	find -type f -exec sed -i -e "s/-lXp //g" {} +
-	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
-	# Unbundle imcat
-	sed -e "s/ imcat / /g" \
-		-i Makefile.INCLUDE || die "Could not edit includes files."
-	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
-		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
-		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-		-i Makefile || die "Could not edit Makefile"
-		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
-		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
-	default
-}
-
-src_compile() {
-	emake -j1 all plugins suma_exec
-}
-
-src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
-	emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
-	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}"
-	done
-}

diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-22.0.03.ebuild
similarity index 72%
rename from sci-biology/afni/afni-20.1.16.ebuild
rename to sci-biology/afni/afni-22.0.03.ebuild
index e2ed432c8..920bf7189 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-22.0.03.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 inherit toolchain-funcs
 
@@ -26,22 +26,18 @@ RDEPEND="dev-libs/expat
 	x11-libs/libXft
 	x11-libs/libXi
 	x11-libs/libXpm
-	x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+	x11-libs/motif
+"
 
 DEPEND="${RDEPEND}
 	app-shells/tcsh"
 
 S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
 
 src_prepare() {
-	eapply "${FILESDIR}/${P}-python.patch" || die
-	find -type f -exec sed -i -e "s/-lXp //g" {} +
+	find -type f -exec sed -i -e "s/-lXp //g" {} + || die
 	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
 	# Unbundle imcat
 	sed -e "s/ imcat / /g" \
@@ -53,10 +49,10 @@ src_prepare() {
 		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
 		-i Makefile || die "Could not edit Makefile"
 		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
+	sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\
 		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
 		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die
 	default
 }
 
@@ -65,9 +61,9 @@ src_compile() {
 }
 
 src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
+	emake INSTALLDIR="${ED}/usr/bin" install install_plugins
 	emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
 	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}"
+		rm "${ED}/usr/bin/${CONFLICT}" || die
 	done
 }

diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild
deleted file mode 100644
index c6e4c669b..000000000
--- a/sci-biology/afni/afni-9999.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3 toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/AFNI/AFNI"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="dev-libs/expat
-	media-libs/glu
-	media-libs/netpbm
-	media-libs/qhull
-	media-video/mpeg-tools
-	sci-libs/gsl
-	sys-devel/llvm:*
-	virtual/jpeg:0
-	x11-libs/libGLw
-	x11-libs/libXft
-	x11-libs/libXi
-	x11-libs/libXpm
-	x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-	app-shells/tcsh"
-
-S="${WORKDIR}/${P}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
-	find -type f -exec sed -i -e "s/-lXp //g" {} +
-	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
-	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
-		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
-		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-		-i Makefile || die "Could not edit Makefile"
-		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
-		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
-	eapply_user
-}
-
-src_compile() {
-	emake -j1 all plugins suma_exec
-}
-
-src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
-	emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
-	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}"
-	done
-}

diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch
deleted file mode 100644
index 24ed98405..000000000
--- a/sci-biology/afni/files/afni-20.1.16-python.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/other_builds/Makefile.linux_fedora_19_64      2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64	2020-10-10 01:15:22.337755934 -0400
-@@ -11,8 +11,6 @@
-
- # ------------------------------
- # python from C
--IPYTHON  = -DSELENIUM_READY -I/usr/include/python2.7
--LDPYTHON = -lpython2.7
-
- # ----------------------------------------------------------------------
- # X configuration

diff --git a/sci-biology/afni/files/afni-20.3.03-python.patch b/sci-biology/afni/files/afni-20.3.03-python.patch
deleted file mode 100644
index 24ed98405..000000000
--- a/sci-biology/afni/files/afni-20.3.03-python.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/other_builds/Makefile.linux_fedora_19_64      2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64	2020-10-10 01:15:22.337755934 -0400
-@@ -11,8 +11,6 @@
-
- # ------------------------------
- # python from C
--IPYTHON  = -DSELENIUM_READY -I/usr/include/python2.7
--LDPYTHON = -lpython2.7
-
- # ----------------------------------------------------------------------
- # X configuration


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/
@ 2022-04-01  7:48 Horea Christian
  0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2022-04-01  7:48 UTC (permalink / raw
  To: gentoo-commits

commit:     da45c12e15c1bfde33d4c8e0919eccec25b426b8
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Apr  1 07:48:43 2022 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Apr  1 07:48:43 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da45c12e

sci-biology/afni: reinstated working versions

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 .../{afni-22.0.03.ebuild => afni-20.1.16.ebuild}   | 26 +++++++++++--------
 .../{afni-22.0.03.ebuild => afni-20.3.03.ebuild}   | 30 ++++++++++++++--------
 sci-biology/afni/afni-22.0.03.ebuild               |  3 ++-
 sci-biology/afni/files/afni-20.1.16-python.patch   | 11 ++++++++
 sci-biology/afni/files/afni-20.3.03-python.patch   | 11 ++++++++
 5 files changed, 58 insertions(+), 23 deletions(-)

diff --git a/sci-biology/afni/afni-22.0.03.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
similarity index 66%
copy from sci-biology/afni/afni-22.0.03.ebuild
copy to sci-biology/afni/afni-20.1.16.ebuild
index 920bf7189..98fdb2397 100644
--- a/sci-biology/afni/afni-22.0.03.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -26,33 +26,37 @@ RDEPEND="dev-libs/expat
 	x11-libs/libXft
 	x11-libs/libXi
 	x11-libs/libXpm
-	x11-libs/motif
-"
+	x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
 
 DEPEND="${RDEPEND}
 	app-shells/tcsh"
 
 S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
 
 src_prepare() {
-	find -type f -exec sed -i -e "s/-lXp //g" {} + || die
+	eapply "${FILESDIR}/${P}-python.patch" || die
+	find -type f -exec sed -i -e "s/-lXp //g" {} +
 	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
 	# Unbundle imcat
 	sed -e "s/ imcat / /g" \
 		-i Makefile.INCLUDE || die "Could not edit includes files."
-	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
+	sed -e "s~CC	 = /usr/bin/gcc -O2 -m64~CC  = $(tc-getCC) \$(CFLAGS)~" \
 		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
-		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
+		-e "s~LD	 = /usr/bin/gcc~LD   = $(tc-getCC)~" \
+		-e "s~AR	 = /usr/bin/ar~AR	= $(tc-getAR)~" \
 		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
 		-i Makefile || die "Could not edit Makefile"
 		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\
+	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
 		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
 		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die
+	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
 	default
 }
 
@@ -61,9 +65,9 @@ src_compile() {
 }
 
 src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" install install_plugins
+	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
 	emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
 	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}" || die
+		rm "${ED}/usr/bin/${CONFLICT}"
 	done
 }

diff --git a/sci-biology/afni/afni-22.0.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
similarity index 65%
copy from sci-biology/afni/afni-22.0.03.ebuild
copy to sci-biology/afni/afni-20.3.03.ebuild
index 920bf7189..fab7446bf 100644
--- a/sci-biology/afni/afni-22.0.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -26,33 +26,41 @@ RDEPEND="dev-libs/expat
 	x11-libs/libXft
 	x11-libs/libXi
 	x11-libs/libXpm
-	x11-libs/motif
-"
+	x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
 
 DEPEND="${RDEPEND}
 	app-shells/tcsh"
 
 S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+#PATCHES=(
+#   "${FILESDIR}/${P}-python.patch"
+#)
 
 src_prepare() {
-	find -type f -exec sed -i -e "s/-lXp //g" {} + || die
+	eapply "${FILESDIR}/${P}-python.patch" || die
+	find -type f -exec sed -i -e "s/-lXp //g" {} +
 	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
 	# Unbundle imcat
 	sed -e "s/ imcat / /g" \
 		-i Makefile.INCLUDE || die "Could not edit includes files."
-	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
+	sed -e "s~CC	 = /usr/bin/gcc -O2 -m64~CC	 = $(tc-getCC) \$(CFLAGS)~" \
 		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
-		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
+		-e "s~LD	 = /usr/bin/gcc~LD	 = $(tc-getCC)~" \
+		-e "s~AR	 = /usr/bin/ar~AR	 = $(tc-getAR)~" \
 		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
 		-i Makefile || die "Could not edit Makefile"
 		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\
+	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
 		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
 		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die
+	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
 	default
 }
 
@@ -61,9 +69,9 @@ src_compile() {
 }
 
 src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" install install_plugins
+	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
 	emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
 	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}" || die
+		rm "${ED}/usr/bin/${CONFLICT}"
 	done
 }

diff --git a/sci-biology/afni/afni-22.0.03.ebuild b/sci-biology/afni/afni-22.0.03.ebuild
index 920bf7189..9e831b018 100644
--- a/sci-biology/afni/afni-22.0.03.ebuild
+++ b/sci-biology/afni/afni-22.0.03.ebuild
@@ -11,7 +11,8 @@ SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+# fully broken due to upstream cmake migration
+KEYWORDS=""
 IUSE=""
 
 RDEPEND="dev-libs/expat

diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch
new file mode 100644
index 000000000..8c3e859f5
--- /dev/null
+++ b/sci-biology/afni/files/afni-20.1.16-python.patch
@@ -0,0 +1,11 @@
+--- a/other_builds/Makefile.linux_fedora_19_64      2020-10-09 07:07:58.348874414 -0400
++++ b/other_builds/Makefile.linux_fedora_19_64  2020-10-10 01:15:22.337755934 -0400
+@@ -11,8 +11,6 @@
+
+ # ------------------------------
+ # python from C
+-IPYTHON  = -DSELENIUM_READY -I/usr/include/python2.7
+-LDPYTHON = -lpython2.7
+
+ # ----------------------------------------------------------------------
+ # X configuration

diff --git a/sci-biology/afni/files/afni-20.3.03-python.patch b/sci-biology/afni/files/afni-20.3.03-python.patch
new file mode 100644
index 000000000..8c3e859f5
--- /dev/null
+++ b/sci-biology/afni/files/afni-20.3.03-python.patch
@@ -0,0 +1,11 @@
+--- a/other_builds/Makefile.linux_fedora_19_64      2020-10-09 07:07:58.348874414 -0400
++++ b/other_builds/Makefile.linux_fedora_19_64  2020-10-10 01:15:22.337755934 -0400
+@@ -11,8 +11,6 @@
+
+ # ------------------------------
+ # python from C
+-IPYTHON  = -DSELENIUM_READY -I/usr/include/python2.7
+-LDPYTHON = -lpython2.7
+
+ # ----------------------------------------------------------------------
+ # X configuration


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/
@ 2022-04-03  8:13 Horea Christian
  0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2022-04-03  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     48589a716ae0690d1f7968fa42eb3c8686cef7a8
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Apr  3 08:13:53 2022 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Apr  3 08:13:53 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=48589a71

sci-biology/afni: version patches are identical

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/afni/afni-20.3.03.ebuild             |  2 +-
 sci-biology/afni/afni-22.0.21.ebuild             |  2 +-
 sci-biology/afni/files/afni-20.3.03-python.patch | 11 -----------
 sci-biology/afni/files/afni-22.0.21-python.patch | 13 -------------
 4 files changed, 2 insertions(+), 26 deletions(-)

diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
index a95a34cfb..1cc1a3246 100644
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -40,7 +40,7 @@ BUILD="linux_fedora_19_64"
 BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
 
 src_prepare() {
-	eapply "${FILESDIR}/${P}-python.patch" || die
+	eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
 	find -type f -exec sed -i -e "s/-lXp //g" {} +
 	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
 	# Unbundle imcat

diff --git a/sci-biology/afni/afni-22.0.21.ebuild b/sci-biology/afni/afni-22.0.21.ebuild
index 6694c9525..6d791e6e1 100644
--- a/sci-biology/afni/afni-22.0.21.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -42,7 +42,7 @@ BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
 
 src_prepare() {
 	# more easily applied here than via PATCHES at phase end.
-	eapply "${FILESDIR}/${P}-python.patch" || die
+	eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
 	find -type f -exec sed -i -e "s/-lXp //g" {} + || die
 	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
 	# Unbundle imcat

diff --git a/sci-biology/afni/files/afni-20.3.03-python.patch b/sci-biology/afni/files/afni-20.3.03-python.patch
deleted file mode 100644
index 8c3e859f5..000000000
--- a/sci-biology/afni/files/afni-20.3.03-python.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/other_builds/Makefile.linux_fedora_19_64      2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64  2020-10-10 01:15:22.337755934 -0400
-@@ -11,8 +11,6 @@
-
- # ------------------------------
- # python from C
--IPYTHON  = -DSELENIUM_READY -I/usr/include/python2.7
--LDPYTHON = -lpython2.7
-
- # ----------------------------------------------------------------------
- # X configuration

diff --git a/sci-biology/afni/files/afni-22.0.21-python.patch b/sci-biology/afni/files/afni-22.0.21-python.patch
deleted file mode 100644
index f31cc051b..000000000
--- a/sci-biology/afni/files/afni-22.0.21-python.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/other_builds/Makefile.linux_fedora_19_64 b/other_builds/Makefile.linux_fedora_19_64
-index ebaa9d5..1471081 100644
---- a/other_builds/Makefile.linux_fedora_19_64
-+++ b/other_builds/Makefile.linux_fedora_19_64
-@@ -11,8 +11,6 @@ LGIFTI    = -lexpat
- 
- # ------------------------------
- # python from C
--IPYTHON  = -DSELENIUM_READY -I/usr/include/python2.7
--LDPYTHON = -lpython2.7
- 
- # ----------------------------------------------------------------------
- # X configuration


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/
@ 2024-05-28 17:11 Horea Christian
  0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2024-05-28 17:11 UTC (permalink / raw
  To: gentoo-commits

commit:     0075b0aa4f9993e0bc54e9d627329332555d16e0
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue May 28 17:10:35 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue May 28 17:10:35 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0075b0aa

sci-biology/afni: env variable for AFNI data

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/afni/afni-24.0.08-r2.ebuild | 124 ++++++++++++++++++++++++++++++++
 sci-biology/afni/files/97afni           |   1 +
 2 files changed, 125 insertions(+)

diff --git a/sci-biology/afni/afni-24.0.08-r2.ebuild b/sci-biology/afni/afni-24.0.08-r2.ebuild
new file mode 100644
index 000000000..270100c0b
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r2.ebuild
@@ -0,0 +1,124 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
+SRC_URI="
+	https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+	https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+	https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+	"
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-build/ninja
+	dev-libs/expat
+	dev-libs/glib:2
+	dev-libs/libf2c
+	media-libs/freeglut
+	media-libs/glu
+	media-libs/netpbm
+	media-libs/qhull
+	media-video/mpeg-tools
+	sci-biology/afni-datasets
+	sci-libs/gsl
+	sci-libs/gts
+	sys-devel/llvm:*
+	sys-libs/libomp
+	virtual/jpeg-compat:62
+	x11-libs/libGLw
+	x11-libs/libXft
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXpm
+	x11-libs/libXt
+	x11-libs/motif[-static-libs]
+	"
+DEPEND="
+	${RDEPEND}
+	app-shells/tcsh
+	"
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+	#tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+	tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+	tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+	cmake_src_prepare
+	default
+	}
+
+src_configure() {
+	if use !whirlgif; then
+		eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+	fi
+	export CFLAGS="-pthread ${CFLAGS}"
+	export GIT_REPO_VERSION=3.0.1.1
+	local mycmakeargs=(
+		-DLIBDIR=/usr/$(get_libdir)
+		-DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+		-DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+		-DCOMP_COREBINARIES=ON
+		-DUSE_SYSTEM_NIFTI=OFF
+		-DUSE_SYSTEM_GIFTI=OFF
+		-DUSE_SYSTEM_XMHTML=OFF
+		-DUSE_SYSTEM_GTS=ON
+		-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+		-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+		-DCOMP_GUI=ON
+		-DCOMP_PLUGINS=ON
+		-DUSE_OMP=ON
+		-DCOMP_PYTHON=OFF
+		-DUSE_SYSTEM_F2C=ON
+	)
+	tc-export CC
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	pushd src/python_scripts
+		distutils-r1_src_compile
+	popd
+}
+
+src_install() {
+	cmake_src_install
+	pushd src/python_scripts
+		distutils-r1_src_install
+	popd
+	cd "${D}"
+	rm usr/bin/mpeg_encode
+	doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use afni binaries from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}

diff --git a/sci-biology/afni/files/97afni b/sci-biology/afni/files/97afni
new file mode 100644
index 000000000..dbf463f47
--- /dev/null
+++ b/sci-biology/afni/files/97afni
@@ -0,0 +1 @@
+export AFNI_ATLAS_PATH=/usr/share/afni-datasets


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/
@ 2024-06-06 23:05 Horea Christian
  0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2024-06-06 23:05 UTC (permalink / raw
  To: gentoo-commits

commit:     5307342730267714f7019d62f77b2d9bf7624d8c
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jun  6 23:04:29 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jun  6 23:05:15 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=53073427

sci-biology/afni: add 24.1.15, 24.1.16

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/afni/afni-24.1.15.ebuild              | 125 +++++++++++++++++++++
 sci-biology/afni/afni-24.1.16.ebuild              | 127 ++++++++++++++++++++++
 sci-biology/afni/files/afni-24.1.16-niftiio.patch |  27 +++++
 3 files changed, 279 insertions(+)

diff --git a/sci-biology/afni/afni-24.1.15.ebuild b/sci-biology/afni/afni-24.1.15.ebuild
new file mode 100644
index 000000000..12d6c8f87
--- /dev/null
+++ b/sci-biology/afni/afni-24.1.15.ebuild
@@ -0,0 +1,125 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
+SRC_URI="
+	https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+	https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+	https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+	"
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-build/ninja
+	dev-libs/expat
+	dev-libs/glib:2
+	dev-libs/libf2c
+	media-libs/freeglut
+	media-libs/glu
+	media-libs/netpbm
+	media-libs/qhull
+	media-video/mpeg-tools
+	sci-biology/afni-datasets
+	sci-libs/gsl
+	sci-libs/gts
+	sys-devel/llvm:*
+	sys-libs/libomp
+	virtual/jpeg-compat:62
+	x11-libs/libGLw
+	x11-libs/libXft
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXpm
+	x11-libs/libXt
+	x11-libs/motif[-static-libs]
+	"
+DEPEND="
+	${RDEPEND}
+	app-shells/tcsh
+	"
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+	#tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+	tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+	tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+	cmake_src_prepare
+	default
+	}
+
+src_configure() {
+	if use !whirlgif; then
+		eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+	fi
+	# Fix AFNI version, no better way seemed to work
+	sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake
+	export CFLAGS="-pthread ${CFLAGS}"
+	local mycmakeargs=(
+		-DLIBDIR=/usr/$(get_libdir)
+		-DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+		-DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+		-DCOMP_COREBINARIES=ON
+		-DUSE_SYSTEM_NIFTI=OFF
+		-DUSE_SYSTEM_GIFTI=OFF
+		-DUSE_SYSTEM_XMHTML=OFF
+		-DUSE_SYSTEM_GTS=ON
+		-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+		-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+		-DCOMP_GUI=ON
+		-DCOMP_PLUGINS=ON
+		-DUSE_OMP=ON
+		-DCOMP_PYTHON=OFF
+		-DUSE_SYSTEM_F2C=ON
+	)
+	tc-export CC
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	pushd src/python_scripts
+		distutils-r1_src_compile
+	popd
+}
+
+src_install() {
+	cmake_src_install
+	pushd src/python_scripts
+		distutils-r1_src_install
+	popd
+	cd "${D}"
+	rm usr/bin/mpeg_encode
+	doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use afni binaries from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}

diff --git a/sci-biology/afni/afni-24.1.16.ebuild b/sci-biology/afni/afni-24.1.16.ebuild
new file mode 100644
index 000000000..0759d30a0
--- /dev/null
+++ b/sci-biology/afni/afni-24.1.16.ebuild
@@ -0,0 +1,127 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="f24bec503f1a5d501c0413c1bb8aa3d6e04aebda"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
+SRC_URI="
+	https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+	https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+	https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+	"
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-build/ninja
+	dev-libs/expat
+	dev-libs/glib:2
+	dev-libs/libf2c
+	media-libs/freeglut
+	media-libs/glu
+	media-libs/netpbm
+	media-libs/qhull
+	media-video/mpeg-tools
+	sci-biology/afni-datasets
+	sci-libs/gsl
+	sci-libs/gts
+	sys-devel/llvm:*
+	sys-libs/libomp
+	virtual/jpeg-compat:62
+	x11-libs/libGLw
+	x11-libs/libXft
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXpm
+	x11-libs/libXt
+	x11-libs/motif[-static-libs]
+	"
+DEPEND="
+	${RDEPEND}
+	app-shells/tcsh
+	"
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+PATCHES=("${FILESDIR}/afni-24.1.16-niftiio.patch")
+
+	#tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+	# We need a name without the hash to reference in patches
+	mv "${WORKDIR}/nifti_clib-${NIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/nifti_clib_from_github"
+	mv "${WORKDIR}/gifti_clib-${GIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github"
+	cmake_src_prepare
+}
+
+src_configure() {
+	if use !whirlgif; then
+		eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+	fi
+	# Fix AFNI version, no better way seemed to work
+	sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake
+	export CFLAGS="-pthread ${CFLAGS}"
+	local mycmakeargs=(
+		-DLIBDIR=/usr/$(get_libdir)
+		-DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+		-DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+		-DCOMP_COREBINARIES=ON
+		-DUSE_SYSTEM_NIFTI=OFF
+		-DUSE_SYSTEM_GIFTI=OFF
+		-DUSE_SYSTEM_XMHTML=OFF
+		-DUSE_SYSTEM_GTS=ON
+		-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/afni-AFNI_24.1.16/nifti_clib_from_github"
+		-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github"
+		-DCOMP_GUI=ON
+		-DCOMP_PLUGINS=ON
+		-DUSE_OMP=ON
+		-DCOMP_PYTHON=OFF
+		-DUSE_SYSTEM_F2C=ON
+	)
+	tc-export CC
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	pushd src/python_scripts
+		distutils-r1_src_compile
+	popd
+}
+
+src_install() {
+	cmake_src_install
+	pushd src/python_scripts
+		distutils-r1_src_install
+	popd
+	cd "${D}"
+	rm usr/bin/mpeg_encode
+	doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use afni binaries from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}

diff --git a/sci-biology/afni/files/afni-24.1.16-niftiio.patch b/sci-biology/afni/files/afni-24.1.16-niftiio.patch
new file mode 100644
index 000000000..a4eb35435
--- /dev/null
+++ b/sci-biology/afni/files/afni-24.1.16-niftiio.patch
@@ -0,0 +1,27 @@
+From 05dbcd2659fa6177b221a2686300036e4ae435d6 Mon Sep 17 00:00:00 2001
+From: Yaroslav Halchenko <debian@onerussian.com>
+Date: Mon, 3 Jun 2024 19:28:21 -0400
+Subject: [PATCH] Announce niftiio as PRIVATE for linking to prevent
+ propagating linking against it
+
+I am just a messanger from the cmake-wise @leej3 at
+https://github.com/afni/afni/issues/639#issuecomment-2145703256
+
+Supposedly closes #639
+---
+ src/nifti/nifticdf/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/nifti/nifticdf/CMakeLists.txt b/src/nifti/nifticdf/CMakeLists.txt
+index 473be7e3be..01b18a14d8 100644
+--- a/nifti_clib_from_github/nifticdf/CMakeLists.txt
++++ b/nifti_clib_from_github/nifticdf/CMakeLists.txt
+@@ -8,7 +8,7 @@ set_target_properties(
+     "${CMAKE_CURRENT_LIST_DIR}/nifticdf.h"
+   )
+ target_compile_options(${NIFTI_CDFLIB_NAME} PRIVATE "-D__COMPILE_UNUSED_FUNCTIONS__")
+-target_link_libraries(${NIFTI_CDFLIB_NAME} PUBLIC ${NIFTI_PACKAGE_PREFIX}niftiio)
++target_link_libraries(${NIFTI_CDFLIB_NAME} PRIVATE ${NIFTI_PACKAGE_PREFIX}niftiio)
+ get_lib_version_vars("nifticdf_version.h" NIFTICDF_VERSION NIFTICDF_MAJOR_VERSION)
+ if(BUILD_SHARED_LIBS)
+     set_target_properties(${NIFTI_CDFLIB_NAME}


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